Calcium in PDB 1wmz: Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine

The structure of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine, PDB code: 1wmz was solved by H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, T.Hatakeyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.81 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.580, 52.240, 136.590, 90.00, 91.66, 90.00
R / Rfree (%)	15.8 / 18.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine (pdb code 1wmz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine, PDB code: 1wmz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:20.2 occ:1.00 O A:GLU109 2.4 20.2 1.0 O A:HOH549 2.4 21.8 1.0 OD2 A:ASP77 2.4 21.0 1.0 OE2 A:GLU81 2.4 26.1 1.0 OE1 A:GLU81 2.6 24.4 1.0 OD1 A:ASP77 2.6 18.9 1.0 OD1 A:ASN104 2.6 19.8 1.0 OD2 A:ASP110 2.7 28.1 1.0 CD A:GLU81 2.8 23.7 1.0 CG A:ASP77 2.9 22.7 1.0 C A:GLU109 3.4 20.9 1.0 CG A:ASN104 3.4 20.9 1.0 CG A:ASP110 3.7 27.2 1.0 CA A:ASP110 3.7 21.6 1.0 N A:ASP110 3.9 21.0 1.0 CA A:CA203 4.0 41.8 1.0 CB A:ASN104 4.0 20.2 1.0 CB A:ASP110 4.1 23.0 1.0 ND2 A:ASN104 4.3 18.7 1.0 CG A:GLU81 4.3 25.5 1.0 CB A:ASP77 4.4 21.4 1.0 CZ A:PHE84 4.4 20.9 1.0 CA A:ASN104 4.5 20.4 1.0 CA A:GLU109 4.6 20.6 1.0 OD2 A:ASP124 4.6 17.7 1.0 O A:ASP77 4.7 22.8 1.0 N A:GLU109 4.7 21.8 1.0 N A:GLY82 4.7 24.7 1.0 O A:HOH506 4.7 29.1 1.0 OD1 A:ASP110 4.8 34.6 1.0 O A:HOH553 4.8 21.9 1.0 O A:HOH539 4.9 30.4 1.0 CE2 A:PHE84 4.9 20.1 1.0 CA A:GLU81 4.9 26.9 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:18.5 occ:1.00 OE1 A:GLU109 2.2 17.8 1.0 OD1 A:ASP124 2.4 18.8 1.0 O A:ASP124 2.5 18.6 1.0 OD2 A:ASP103 2.5 17.7 1.0 OD1 A:ASN123 2.5 18.8 1.0 O4 A:NGA501 2.5 18.7 1.0 O3 A:NGA501 2.5 19.2 1.0 OE1 A:GLN101 2.6 18.1 1.0 CD A:GLU109 3.3 15.1 1.0 CG A:ASP124 3.4 20.2 1.0 CD A:GLN101 3.4 17.7 1.0 C3 A:NGA501 3.4 17.9 1.0 C4 A:NGA501 3.5 18.6 1.0 CG A:ASN123 3.5 18.4 1.0 CG A:ASP103 3.5 23.6 1.0 C A:ASP124 3.6 18.3 1.0 OE2 A:GLU109 3.7 18.8 1.0 NE2 A:GLN101 3.8 21.8 1.0 N A:ASP124 3.8 17.7 1.0 OD1 A:ASP103 3.9 22.1 1.0 ND2 A:ASN123 3.9 17.3 1.0 OD2 A:ASP124 4.0 17.7 1.0 CA A:ASP124 4.1 18.5 1.0 C2 A:NGA501 4.2 18.5 1.0 CB A:ASP124 4.3 18.3 1.0 N A:ASP103 4.4 21.6 1.0 CG A:GLU109 4.5 18.6 1.0 CB A:GLU109 4.6 19.6 1.0 CG A:GLN101 4.7 19.9 1.0 CB A:TRP105 4.7 20.5 1.0 N A:ASN125 4.7 18.4 1.0 CB A:ASP103 4.7 20.3 1.0 C5 A:NGA501 4.7 20.0 1.0 CB A:ASN123 4.8 17.7 1.0 C A:ASN123 4.8 18.8 1.0 N A:TRP105 4.9 19.5 1.0 N A:ASN104 4.9 21.2 1.0 CA A:ASP103 5.0 21.6 1.0 CA A:ASN123 5.0 17.6 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:41.8 occ:1.00 O A:HOH506 2.2 29.1 1.0 OD2 A:ASP110 2.4 28.1 1.0 OE2 A:GLU81 2.6 26.1 1.0 CG A:ASP110 3.0 27.2 1.0 OD1 A:ASP110 3.1 34.6 1.0 CD A:GLU81 3.7 23.7 1.0 CA A:CA201 4.0 20.2 1.0 O A:ASP77 4.2 22.8 1.0 OD1 A:ASN104 4.3 19.8 1.0 CB A:GLU81 4.3 26.8 1.0 CB A:ASP110 4.4 23.0 1.0 CG A:GLU81 4.4 25.5 1.0 O A:LYS78 4.6 29.5 1.0 OD1 A:ASP77 4.6 18.9 1.0 OE1 A:GLU81 4.7 24.4 1.0 O A:ASN107 4.7 24.6 1.0 CA A:LYS78 4.8 27.2 1.0 CA A:GLU81 4.8 26.9 1.0 OD2 A:ASP77 4.9 21.0 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:12.2 occ:1.00 O B:HOH593 2.3 12.3 1.0 OD2 B:ASP77 2.4 10.7 1.0 OD1 B:ASP110 2.5 13.4 1.0 OE1 B:GLU81 2.5 16.0 1.0 O B:GLU109 2.5 12.5 1.0 OE2 B:GLU81 2.5 13.5 1.0 OD1 B:ASN104 2.5 12.7 1.0 OD1 B:ASP77 2.6 11.9 1.0 CD B:GLU81 2.8 13.2 1.0 CG B:ASP77 2.9 12.3 1.0 CG B:ASN104 3.3 13.2 1.0 C B:GLU109 3.5 11.9 1.0 CG B:ASP110 3.5 14.8 1.0 CA B:ASP110 3.8 11.4 1.0 CA B:CA203 3.9 28.5 1.0 CB B:ASN104 4.0 12.3 1.0 N B:ASP110 4.0 11.4 1.0 CB B:ASP110 4.1 11.9 1.0 ND2 B:ASN104 4.2 15.1 1.0 CG B:GLU81 4.3 13.0 1.0 CZ B:PHE84 4.3 12.6 1.0 CB B:ASP77 4.4 10.1 1.0 CA B:ASN104 4.5 12.8 1.0 OD2 B:ASP110 4.5 27.0 1.0 CA B:GLU109 4.6 12.1 1.0 O B:HOH574 4.6 13.7 1.0 N B:GLU109 4.6 13.6 1.0 OD2 B:ASP124 4.6 11.6 1.0 N B:GLY82 4.7 14.8 1.0 CE2 B:PHE84 4.7 11.8 1.0 O B:HOH594 4.8 13.8 1.0 O B:HOH580 4.8 18.8 1.0 CA B:GLU81 4.9 13.4 1.0 O B:ASP77 4.9 11.9 1.0 CB B:GLU81 5.0 14.1 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:11.6 occ:1.00 OD1 B:ASP124 2.3 10.5 1.0 O B:ASP124 2.4 12.0 1.0 OE1 B:GLU109 2.4 12.2 1.0 OE1 B:GLN101 2.5 11.3 1.0 OD1 B:ASN123 2.5 11.5 1.0 O3 B:A2G502 2.5 12.3 1.0 OD2 B:ASP103 2.5 12.0 1.0 O4 B:A2G502 2.6 11.5 1.0 CG B:ASP124 3.4 12.4 1.0 CD B:GLU109 3.4 13.4 1.0 CD B:GLN101 3.4 13.8 1.0 C3 B:A2G502 3.4 15.6 1.0 CG B:ASP103 3.4 14.7 1.0 CG B:ASN123 3.4 10.4 1.0 C4 B:A2G502 3.5 11.8 1.0 C B:ASP124 3.5 10.8 1.0 OE2 B:GLU109 3.7 12.6 1.0 N B:ASP124 3.8 10.9 1.0 OD1 B:ASP103 3.8 14.8 1.0 ND2 B:ASN123 3.8 10.5 1.0 NE2 B:GLN101 3.8 13.8 1.0 CA B:ASP124 4.0 10.7 1.0 OD2 B:ASP124 4.1 11.6 1.0 C2 B:A2G502 4.2 12.7 1.0 N B:ASP103 4.2 12.2 1.0 CB B:ASP124 4.2 11.2 1.0 CG B:GLN101 4.6 12.5 1.0 CG B:GLU109 4.6 13.4 1.0 CB B:ASP103 4.6 12.6 1.0 N B:ASN125 4.6 11.4 1.0 CB B:GLU109 4.7 12.4 1.0 CB B:ASN123 4.8 10.1 1.0 C B:ASN123 4.8 10.8 1.0 C5 B:A2G502 4.8 14.0 1.0 CB B:TRP105 4.8 15.7 1.0 CA B:ASP103 4.8 11.9 1.0 N B:ASN104 4.9 12.1 1.0 N B:TRP105 4.9 13.3 1.0 CA B:ASN123 5.0 10.8 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:28.5 occ:1.00 O B:HOH574 2.2 13.7 1.0 OD1 B:ASP110 2.5 13.4 1.0 OE2 B:GLU81 2.5 13.5 1.0 O B:HOH583 2.5 23.8 1.0 OD2 B:ASP110 2.7 27.0 1.0 CG B:ASP110 2.9 14.8 1.0 CD B:GLU81 3.7 13.2 1.0 CA B:CA201 3.9 12.2 1.0 OD1 B:ASN104 4.3 12.7 1.0 CB B:GLU81 4.3 14.1 1.0 CB B:ASP110 4.4 11.9 1.0 CG B:GLU81 4.4 13.0 1.0 O B:ASP77 4.6 11.9 1.0 O B:ASN107 4.6 20.4 1.0 OE1 B:GLU81 4.6 16.0 1.0 OD1 B:ASP77 4.6 11.9 1.0 O B:LYS78 4.8 12.6 1.0 CA B:GLU81 4.9 13.4 1.0 O B:HOH607 4.9 32.4 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:12.2 occ:1.00 O C:HOH588 2.4 13.9 1.0 OD2 C:ASP77 2.4 12.2 1.0 O C:GLU109 2.4 12.2 1.0 OE2 C:GLU81 2.5 14.4 1.0 OE1 C:GLU81 2.5 15.0 1.0 OD2 C:ASP110 2.5 17.9 1.0 OD1 C:ASN104 2.6 13.7 1.0 OD1 C:ASP77 2.6 12.9 1.0 CD C:GLU81 2.8 14.0 1.0 CG C:ASP77 2.9 12.5 1.0 CG C:ASN104 3.3 12.3 1.0 C C:GLU109 3.4 12.1 1.0 CG C:ASP110 3.6 15.8 1.0 CA C:ASP110 3.8 12.2 1.0 CA C:CA203 3.9 29.0 1.0 CB C:ASN104 4.0 13.4 1.0 N C:ASP110 4.0 12.2 1.0 CB C:ASP110 4.2 14.5 1.0 ND2 C:ASN104 4.2 14.0 1.0 CG C:GLU81 4.3 14.6 1.0 CZ C:PHE84 4.4 13.3 1.0 CB C:ASP77 4.4 12.1 1.0 CA C:ASN104 4.5 12.2 1.0 OD1 C:ASP110 4.6 27.1 1.0 OD2 C:ASP124 4.6 12.7 1.0 CA C:GLU109 4.6 12.2 1.0 O C:HOH521 4.6 18.8 1.0 N C:GLU109 4.6 12.7 1.0 O C:HOH587 4.7 16.0 1.0 N C:GLY82 4.8 16.1 1.0 O C:ASP77 4.9 13.0 1.0 CE2 C:PHE84 4.9 14.5 1.0 O C:HOH579 4.9 23.4 1.0 CA C:GLU81 4.9 13.8 1.0 CB C:GLU81 5.0 14.7 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:11.4 occ:1.00 OE1 C:GLU109 2.3 12.5 1.0 OD1 C:ASP124 2.3 11.8 1.0 OD1 C:ASN123 2.4 11.7 1.0 O4 C:NGA503 2.5 10.8 1.0 OD2 C:ASP103 2.5 10.4 1.0 O C:ASP124 2.5 10.9 1.0 OE1 C:GLN101 2.5 11.3 1.0 O3 C:NGA503 2.6 11.8 1.0 CD C:GLU109 3.3 11.3 1.0 CG C:ASP124 3.4 11.6 1.0 CD C:GLN101 3.4 12.0 1.0 C3 C:NGA503 3.4 12.6 1.0 C4 C:NGA503 3.4 12.3 1.0 CG C:ASN123 3.5 12.4 1.0 CG C:ASP103 3.5 12.4 1.0 C C:ASP124 3.6 10.7 1.0 OE2 C:GLU109 3.7 12.3 1.0 N C:ASP124 3.8 9.9 1.0 NE2 C:GLN101 3.8 14.7 1.0 ND2 C:ASN123 3.9 11.3 1.0 OD1 C:ASP103 3.9 11.7 1.0 CA C:ASP124 4.0 10.4 1.0 OD2 C:ASP124 4.1 12.7 1.0 C2 C:NGA503 4.1 11.2 1.0 CB C:ASP124 4.3 10.4 1.0 N C:ASP103 4.3 13.9 1.0 CG C:GLU109 4.5 11.4 1.0 CG C:GLN101 4.6 11.5 1.0 CB C:GLU109 4.6 12.4 1.0 CB C:ASP103 4.7 13.7 1.0 C5 C:NGA503 4.7 15.0 1.0 N C:ASN125 4.7 10.7 1.0 CB C:TRP105 4.7 12.7 1.0 CB C:ASN123 4.7 10.3 1.0 C C:ASN123 4.8 10.1 1.0 N C:ASN104 4.8 13.7 1.0 N C:TRP105 4.8 13.3 1.0 CA C:ASP103 4.9 13.9 1.0 CA C:ASN123 5.0 9.5 1.0 N2 C:NGA503 5.0 12.1 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:29.0 occ:1.00 O C:HOH521 2.1 18.8 1.0 O C:HOH603 2.5 24.4 1.0 OD2 C:ASP110 2.5 17.9 1.0 OE2 C:GLU81 2.5 14.4 1.0 OD1 C:ASP110 2.7 27.1 1.0 CG C:ASP110 3.0 15.8 1.0 CD C:GLU81 3.7 14.0 1.0 CA C:CA201 3.9 12.2 1.0 CB C:GLU81 4.3 14.7 1.0 OD1 C:ASN104 4.3 13.7 1.0 CG C:GLU81 4.4 14.6 1.0 O C:ASP77 4.4 13.0 1.0 CB C:ASP110 4.4 14.5 1.0 O C:HOH605 4.5 33.1 1.0 OD1 C:ASP77 4.6 12.9 1.0 OE1 C:GLU81 4.6 15.0 1.0 O C:LYS78 4.7 15.1 1.0 CA C:GLU81 4.7 13.8 1.0 O C:ASN107 4.8 17.1 1.0 CA C:LYS78 4.9 15.5 1.0 OD2 C:ASP77 4.9 12.2 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of C-Type Lectin Cel-I Complexed with N- Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:17.2 occ:1.00 O D:HOH568 2.4 15.8 1.0 O D:GLU109 2.4 16.8 1.0 OD1 D:ASN104 2.5 19.5 1.0 OD2 D:ASP77 2.5 16.0 1.0 OE1 D:GLU81 2.5 17.4 1.0 OE2 D:GLU81 2.6 18.0 1.0 OD1 D:ASP110 2.6 20.4 1.0 OD1 D:ASP77 2.6 17.2 1.0 CD D:GLU81 2.8 16.9 1.0 CG D:ASP77 3.0 18.6 1.0 CG D:ASN104 3.3 22.1 1.0 C D:GLU109 3.4 17.1 1.0 CG D:ASP110 3.6 20.0 1.0 CA D:ASP110 3.8 15.5 1.0 CA D:CA203 3.8 42.4 1.0 CB D:ASN104 4.0 22.0 1.0 N D:ASP110 4.0 16.1 1.0 ND2 D:ASN104 4.1 20.0 1.0 CB D:ASP110 4.2 15.6 1.0 CG D:GLU81 4.3 16.4 1.0 CZ D:PHE84 4.4 18.6 1.0 CA D:ASN104 4.4 22.4 1.0 CB D:ASP77 4.5 16.7 1.0 CA D:GLU109 4.6 18.9 1.0 N D:GLU109 4.6 20.3 1.0 OD2 D:ASP110 4.6 27.7 1.0 O D:HOH520 4.6 17.5 1.0 OD2 D:ASP124 4.7 18.5 1.0 N D:GLY82 4.7 17.7 1.0 O D:HOH569 4.8 21.3 1.0 CE2 D:PHE84 4.8 18.9 1.0 O D:HOH543 4.9 21.2 1.0 CA D:GLU81 5.0 17.0 1.0

H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, T.Hatakeyama. Characteristic Recognition of N-Acetylgalactosamine By An Invertebrate C-Type Lectin, Cel-I, Revealed By X-Ray Crystallographic Analysis J.Biol.Chem. V. 279 45219 2004.
ISSN: ISSN 0021-9258
PubMed: 15319425
DOI: 10.1074/JBC.M408840200